five selfish reasons to work reproducibly
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- 1. Florian Markowetz CRUK Cambridge Institute www.markowetzlab.org 5 selfish reasons to work reproducibly More publications, more grants, more awesome!
- 2. Systems Genetics of Cancer Genetic variation In people In tumours In clones Phenotypic variation Tumour subtypes Aggressiveness Survival
- 3. Cancer genome Evolution Cancer tissue Context Cancer genome Function Ines Wei Edith Geo Ke Anne Joe Leon Andy Amanda
- 4. Science miracles
- 5. How Bright Promise in Cancer Testing Fell Apart New York Times, July 7, 2011
- 6. SlidesbyKeithBaggerly
- 7. SlidesbyKeithBaggerly
- 8. SlidesbyKeithBaggerly
- 9. Baggerly & Coombes, AOAS 2009
- 10. SlidesbyKeithBaggerly
- 11. http://videolectures.net/ cancerbioinformatics2010_baggerly_irrh/
- 12. Reproducible Research Its the right thing to do! The world would be a better place if everyone did it! Its the foundation of Science! Its the honourable thing to do!
- 13. Reproducibility helps to avoid disaster
- 14. Weak StrongPhenotype Step 1 Step 2 Hits Knock-down Known pathway members New RNAi Hits Compare expression phenotypes by NEMs NFB ? Anatomy of the NFB pathway
- 15. What a nice result!
- 16. What a nice result!
- 17. A project is more than a beautiful result!
- 18. Starting with reproducibility early helps saving time later
- 19. Reproducibility helps writing papers
- 20. Why is well-documented and easily accessible code+data useful? Easy to look up numbers and put them in manuscript Be confident your figures and tables are up-to-date Numbers and result automatically update when data change. It is engaging and more eyes can look over the analysis. Easier to spot mistakes.
- 21. Why is well-documented and easily accessible code+data useful? Easy to look up numbers and put them in manuscript Be confident your figures and tables are up-to-date Numbers and result automatically update when data change. It is engaging and more eyes can look over the analysis. Easier to spot mistakes.
- 22. Reproducibility helps arguing with reviewers
- 23. A very engaged reviewer Reviewer: I downloaded the authors data and tried out a variation of their analysis which gave an insignificant result We: Thank you, the reason is XXX and if you do YYY everything is fine.
- 24. Reproducibility enables continuity
- 25. I am so busy, I cant remember all the details of all my projects
- 26. I did this analysis 6 months ago. Of course I cant remember all the details any more
- 27. My PI said I should continue the project of a previous postdoc. But that postdoc is long gone and hasnt saved any scripts or data.
- 28. Reproducibility helps to build your reputation
- 29. http://www.sciencemag.org/content/348/6242/1422/F1.large.jpg
- 30. Mind your own business! I document my data the way I want!
- 31. Excel works just fine. I dont need any fancy R or Python or whatever.
- 32. Sounds alright, but my code and data are spread over so many hard drives and directories that it would just be too much work to collect them all in one place
- 33. My field is very competitive and I cant risk wasting time
- 34. We can always sort out the code and data after submission
- 35. Its only the result that matters!
- 36. Id rather do real science than tidy up my data
- 37. 5 selfish reasons to work reproducibly 1. Avoid disaster 2. Easier to write papers 3. Easier to talk to reviewers 4. Continuity of your work/in the lab 5. Reputation
- 38. When do you need to worry about reproducibility? Before you start the project While you do the analysis When you write the paper When you co-author a paper When you review a paper
- 39. When do you need to worry about reproducibility? Before you start the project While you do the analysis When you write the paper When you co-author a paper When you review a paper
- 40. Scientific SOFT SKILLS Organization of project Tidy data Tidy code Control over tools Documentation Reproducibility project data code analysis paper Lessclickingandpasting, morescriptingandcoding
- 41. Reproducibility is important for Phd students Postdocs PIs Learn tools and apply in daily work! Create aculture of reproducibilityin your lab!
- 42. 5 selfish reasons to work reproducibly 1. Avoid disaster 2. Easier to write papers 3. Easier to talk to reviewers 4. Continuity of your work/in the lab 5. Reputation